Commander Stalin is a free, open source real-time strategy based on Boswars game for Windows and Linux.
Warzone 2100 is a free, real-time strategy and real-time tactics hybrid computer game for Windows, Linux and Mac OSX which offers campaign, tutorial, multi-player and single-player skirmish game modes, unit designer, unit experience system, and everything you would expect from a modern RTS game.
Glest is a free 3D real-time strategy game for Windows and Linux, where you control the armies of two different factions: Tech, which is mainly composed of warriors and mechanical devices, and Magic, that prefers mages and summoned creatures in the battlefield.
The free software community makes games, too. Among the more well-known ones is the Battle for Wesnoth — a turn-based strategy game with a fantasy setting. It doesn’t have shiny 3D graphics or cut-scenes, but it is an interesting and original game and is fun to play. This game is often simply called “Wesnoth”, and the package name is “wesnoth”.